While Donegal - who also lost influential wing-back Ryan McHugh through injury - needed quick scores after the restart, O'Shea and David Clifford extended Kerry's lead to nine points to leave the Tir Chonaill men with a mountain to climb.
But through five Murphy frees and Conor O'Donnell (2) and Shane O'Donnell's scores from play, Donegal outscored Kerry 0-8 to 0-3 from there to narrow the arrears to just four points with 15 minutes left.
That was as close as Donegal got, however, as Seanie O'Shea's two-point free and a fisted score from the excellent Paudie Clifford pushed Kerry clear once more.
While Donegal desperately scrambled for late inspiration, they had only a Daire O Baoill score to show for their efforts before David Clifford's point was followed by Joe O'Connor lashing the ball high into Shaun Patton's net.
O'Connor's strike capped a fine Kerry performance and completed a clean sweep of wins over Ulster opposition in the knockout stages after victories over Cavan, Armagh and Tyrone.
When the hooter sounded and O'Shea booted the ball into the crowd to spark wild celebrations among the Kerry fans, the Kingdom players celebrated jubilantly on the pitch after adding the Sam Maguire to their National League and Munster titles this year.
In a stark emotional contrast, however, the Donegal players fell to their knees as a first All-Ireland final appearance in 11 years ended in heartache.
Kerry scorers: David Clifford 0-9 (3 2pt), Seanie O'Shea 0-6 (2 2ptf, 1f), Paudie Clifford 0-3 (1 2pt), Gavin White and Dylan Geaney 0-3 each, Sean O'Brien 0-2, Joe O'Connor 1-0.
Donegal scorers: Michael Murphy 0-8 (6f), Conor O'Donnell 0-4, Oisin Gallen 0-3, Shane O'Donnell 0-2, Caolan McGonagle 0-1 and Daire O Baoill 0-1 each.